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Bio-thaumaturge: 'Life-upon-magician' is a pretty accurate translation. Term pilfered from China Miéville (decent writer, nice world-builder although a bit derivative... hey i'm writing a fanfic who am i to talk)

Gensokyo: A remote area in eastern Japan, largely forest and mountains. It has been home to many magical creatures since times unknown; some humans live there, but they are mostly second-class citizens and get eaten on occasion. It was sealed away from the outside sometime in the 19th century (probably 1884), and now the only ways to enter are to visit the nearly derelict Hakurei Shrine, be dragged in by a bored and mischievous Yukari Yakumo, or be a member of the Han family.

Good medicine tastes bad: In-joke. Play "Embodiment of Scarlet Devil" using Reimu Hakurei.

Hachiman: Japanese god of war. When mortal, he was Emperor Oujin, the earliest emperor generally agreed to have existed (in the 5th century) as more then a legend or insignificant local chieftain. Irrelevant to the story.

Hourai (aka P'eng-lai): a legendary mountain, believed to float above the Sea of China. Chinese mythology holds it as a paradise, where the trees have jeweled branches, the bowls of rice and sake never become empty, and people live forever. Japanese mythology does not. ZUN, creator of the Touhou games, calls this place "Psuedo (sic) Paradise."

Kanshi: "Stem-branch." An ancient sixty-year cycle of astrological significance, used to tell time in China and Japan. Plays a pivotal role in "Phantasmagoria of Flower View", but used here just for historical flavor.

Kojiki: A chronicle of Japanese mythology compiled from 680 to 712. One of the earliest written works in the Japanese language. Written in man'yogana.

Lunarian: The race of people who live on the moon. There is little canon information on them, but they look similar to humans, except paler. Eirin Yagokoro and Kaguya Houraisan are the in-game representatives of this race.

Man'yogana: The earliest form of Japanese writing, in which Chinese characters were used to represent the sounds of the Japanese language, largely regardless of their meaning. Almost unreadable to modern Japanese people, due to the massive phonetic drift since its use. Sayuka thought the Nihon Shoki was written in this (a fairly understandable mistake since she can't read Chinese either, AFAIK.)

Nameless book youkai: In-joke from the Touhou serial novel "Curiosities of Lotus Asia." The real 'nameless book youkai' is a girl that Reimu Hakurei beat up and stole a number of books from.

Nihon Shoki: A chronicle of mythology and history compiled around 720, shortly after the Kojiki. It was written in Classical Chinese, as many Japanese works were during that time due to the immaturity of the written language. (The passage given here is actually from the Kojiki, as no translation of the Nihon Shoki exists online that I could reference.)

Scarlet Devil Mansion: The residence of Remilia Scarlet, a vampiress. It and she have no immediate relevance to the story beyond the prologue. However, know that her ability is the control of fate.

T'ang: The dynasty that ruled China from 618 to 907. Sometimes, as in this case, used as a term for the nation itself.

Time of Red Light: What we earthlings call a "lunar eclipse". More on this later.

Trigram: A set of three bars, some or all of which may be broken. Originally represented thrown sticks. Used in sets of two as a divination symbol, and in this story as the Lunarian alphabet (based on the decorations on Eirin's skirt.) See Wikipedia:Bagua (concept)

Umami: The "fifth taste". To humans it means the meaty sensation evoked by MSG. The Lunarian word translated to Sayuka as that, however, refers to the (seemingly desirable) flavor of metals present in many of their foods.

Yagokoro: Means "eight minds."

Yakumo: Means "eight clouds." Incidentally, the same surname taken by Lafcadio Hearn.

Youkai: Literally meaning "strange thing", Gensokyo's youkai are an animalistic race of great physical and magical power. Most lesser youkai will have little to do with humans and indiscriminately attack any who enter their territory; greater youkai are more affable, but remain unpredictable and have a dangerous, playful nature. Created youkai (such as Sayuka, Alice Margatroid, Medicine Melancholy) are well-adjusted compared to the rest of the race, but have a tendency to obsess.